Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.

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Cytochrome c oxidases (Coxs) are the basic energy transducers in the respiratory chain of the majority of aerobic organisms. Coxs studied to date are redox-driven proton-pumping enzymes belonging to one of three subfamilies: A-, B-, and C-type oxidases. The C-type oxidases (cbb3 cytochromes), which are widespread among pathogenic bacteria, are the least understood. In particular, the proton-pumping machinery of these Coxs has not yet been elucidated despite the availability of X-ray structure information. Here, we report the discovery of the first (to our knowledge) sodium-pumping Cox (Scox), a cbb3 cytochrome from the extremely alkaliphilic bacterium Thioalkalivibrio versutus. This finding offers clues to the previously unknown structure of the ionpumping channel in the C-type Coxs and provides insight into the functional properties of this enzyme.@en

The Fourth IPCC Assessment Report concluded that ice sheet flow models, in their current state, were unable to provide accurate forecast for the increase of polar ice sheet discharge and the associated contribution to sea level rise. Since then, the glaciological community has undertaken a huge effort to develop and improve a new generation of ice flow models, and as a result a significant number of new ice sheet models have emerged. Among them is the parallel finite-element model Elmer/Ice, based on the open-source multi-physics code Elmer. It was one of the first full-Stokes models used to make projections for the evolution of the whole Greenland ice sheet for the coming two centuries. Originally developed to solve local ice flow problems of high mechanical and physical complexity, Elmer/Ice has today reached the maturity to solve larger-scale problems, earning the status of an ice sheet model. Here, we summarise almost 10 yr of development performed by different groups. Elmer/Ice solves the full-Stokes equations, for isotropic but also anisotropic ice rheology, resolves the grounding line dynamics as a contact problem, and contains various basal friction laws. Derived fields, like the age of the ice, the strain rate or stress, can also be computed. Elmer/Ice includes two recently proposed inverse methods to infer badly known parameters. Elmer is a highly parallelised code thanks to recent developments and the implementation of a block preconditioned solver for the Stokes system. In this paper, all these components are presented in detail, as well as the numerical performance of the Stokes solver and developments planned for the future.

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